Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1in0a1
C--CCCCCCC--CCHHHHHHHHHHHHHHHCCCHHHCCCCEEEEEECCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCHHHCCCCCCCCCCC

>P1;d1in0a2
CCCCCCCCCCCCCCHHHHHHHHHHHHHH--CC------CCEEEEE--CCEEEEECCCHHHHHHHHHHHHHC--CCCCC---CCCC---CCCC
PSA

>P1;d1in0a1
b--98996a8--46385134006105730882a607c18050605588761515056772272027003600853a195931b27aa3798e

>P1;d1in0a2
a9a9999896931979107401720762--82------9081624--c6403250a47a336501730682--a1818---182a---566b


Translating the sequences
C--CCCCCCC--CCHHHHHHHHHHHHHH**CC******CEEEEEE**CCEEEEEECCHHHHHHHHHHHHHH**HCCCC***CCCC***CCCC
C**CCCCCCC**CCHHHHHHHHHHHHHH--CC------C*EEEEE--CCEEEEE*CCHHHHHHHHHHHHH*--*CCCC---CCCC---CCCC

89963.tem
_________________________________
C--CCCCCCC--CCHHHHHHHHHHHHHH--CC------CEEEEEE--CCEEEEEECCHHHHHHHHHHHHHH--HCCCC---CCCC---CCCC




Structural block scores
1	2	-	3.0	P	  75.0  9.8

3	9	C	5.0	H	  8.5  8.4

10	11	-	3.0	P	  75.0  6.0

12	13	C	5.0	H	  5.0  5.0

14	27	H	5.0	H	  3.3  3.8

28	29	-	3.0	P	  4.0  75.0

30	31	C	5.0	H	  5.0  5.0

32	37	-	3.0	P	  6.2  75.0

39	44	E	4.7	H	  2.7  3.5

45	46	-	3.0	P	  6.5  75.0

47	48	C	5.0	H	  7.5  9.2

49	54	E	4.7	H	  3.0  2.3

55	56	C	5.0	H	  5.5  7.2

57	70	H	4.9	H	  3.2  4.4

71	72	-	3.0	P	  4.0  75.0

74	77	C	5.0	H	  5.9  4.5

78	80	-	3.0	P	  5.7  75.0

81	84	C	5.0	H	  5.4  5.4

85	87	-	3.0	P	  8.0  75.0

88	91	C	5.0	H	  9.6  7.1

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